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Malfatti MC, Antoniali G, Codrich M, Burra S, Mangiapane G, Dalla E, Tell G. New perspectives in cancer biology from a study of canonical and non-canonical functions of base excision repair proteins with a focus on early steps. Mutagenesis 2021; 35:129-149. [PMID: 31858150 DOI: 10.1093/mutage/gez051] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Alterations of DNA repair enzymes and consequential triggering of aberrant DNA damage response (DDR) pathways are thought to play a pivotal role in genomic instabilities associated with cancer development, and are further thought to be important predictive biomarkers for therapy using the synthetic lethality paradigm. However, novel unpredicted perspectives are emerging from the identification of several non-canonical roles of DNA repair enzymes, particularly in gene expression regulation, by different molecular mechanisms, such as (i) non-coding RNA regulation of tumour suppressors, (ii) epigenetic and transcriptional regulation of genes involved in genotoxic responses and (iii) paracrine effects of secreted DNA repair enzymes triggering the cell senescence phenotype. The base excision repair (BER) pathway, canonically involved in the repair of non-distorting DNA lesions generated by oxidative stress, ionising radiation, alkylation damage and spontaneous or enzymatic deamination of nucleotide bases, represents a paradigm for the multifaceted roles of complex DDR in human cells. This review will focus on what is known about the canonical and non-canonical functions of BER enzymes related to cancer development, highlighting novel opportunities to understand the biology of cancer and representing future perspectives for designing new anticancer strategies. We will specifically focus on APE1 as an example of a pleiotropic and multifunctional BER protein.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Silvia Burra
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
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2
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Bensimon A, Koch JP, Francica P, Roth SM, Riedo R, Glück AA, Orlando E, Blaukat A, Aebersold DM, Zimmer Y, Aebersold R, Medová M. Deciphering MET-dependent modulation of global cellular responses to DNA damage by quantitative phosphoproteomics. Mol Oncol 2020; 14:1185-1206. [PMID: 32336009 PMCID: PMC7266272 DOI: 10.1002/1878-0261.12696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 03/18/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence suggests that interference with growth factor receptor tyrosine kinase (RTK) signaling can affect DNA damage response (DDR) networks, with a consequent impact on cellular responses to DNA‐damaging agents widely used in cancer treatment. In that respect, the MET RTK is deregulated in abundance and/or activity in a variety of human tumors. Using two proteomic techniques, we explored how disrupting MET signaling modulates global cellular phosphorylation response to ionizing radiation (IR). Following an immunoaffinity‐based phosphoproteomic discovery survey, we selected candidate phosphorylation sites for extensive characterization by targeted proteomics focusing on phosphorylation sites in both signaling networks. Several substrates of the DDR were confirmed to be modulated by sequential MET inhibition and IR, or MET inhibition alone. Upon combined treatment, for two substrates, NUMA1 S395 and CHEK1 S345, the gain and loss of phosphorylation, respectively, were recapitulated using invivo tumor models by immunohistochemistry, with possible utility in future translational research. Overall, we have corroborated phosphorylation sites at the intersection between MET and the DDR signaling networks, and suggest that these represent a class of proteins at the interface between oncogene‐driven proliferation and genomic stability.
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Affiliation(s)
- Ariel Bensimon
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Switzerland
| | - Jonas P Koch
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Paola Francica
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Selina M Roth
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Rahel Riedo
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Astrid A Glück
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Eleonora Orlando
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Andree Blaukat
- Global Research & Development, Merck KGaA, Darmstadt, Germany
| | - Daniel M Aebersold
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Yitzhak Zimmer
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Switzerland.,Faculty of Science, University of Zürich, Switzerland
| | - Michaela Medová
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
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3
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Garutti M, Pelizzari G, Bartoletti M, Malfatti MC, Gerratana L, Tell G, Puglisi F. Platinum Salts in Patients with Breast Cancer: A Focus on Predictive Factors. Int J Mol Sci 2019; 20:E3390. [PMID: 31295913 PMCID: PMC6678596 DOI: 10.3390/ijms20143390] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/07/2019] [Accepted: 07/08/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) is the most frequent oncologic cause of death among women and the improvement of its treatments is compelling. Platinum salts (e.g., carboplatin, cisplatin, and oxaliplatin) are old drugs still used to treat BC, especially the triple-negative subgroup. However, only a subset of patients see a concrete benefit from these drugs, raising the question of how to select them properly. Therefore, predictive biomarkers for platinum salts in BC still represent an unmet clinical need. Here, we review clinical and preclinical works in order to summarize the current evidence about predictive or putative platinum salt biomarkers in BC. The association between BRCA1/2 gene mutations and platinum sensitivity has been largely described. However, beyond the mutations of these two genes, several other proteins belonging to the homologous recombination pathways have been linked to platinum response, defining the concept of BRCAness. Several works, here reviewed, have tried to capture BRCAness through different strategies, such as homologous recombination deficiency (HRD) score and genetic signatures. Moreover, p53 and its family members (p63 and p73) might also be used as predictors of platinum response. Finally, we describe the mounting preclinical evidence regarding base excision repair deficiency as a possible new platinum biomarker.
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Affiliation(s)
- Mattia Garutti
- U.O.C Oncologia Medica, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Roma, Italy
- Dipartimento di Oncologia Medica, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy
| | - Giacomo Pelizzari
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
- Dipartimento di Oncologia Medica, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy
| | - Michele Bartoletti
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
- Dipartimento di Oncologia Medica, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy
| | | | - Lorenzo Gerratana
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
- Dipartimento di Oncologia Medica, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy
| | - Gianluca Tell
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
| | - Fabio Puglisi
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy.
- Dipartimento di Oncologia Medica, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy.
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4
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Limpose KL, Corbett AH, Doetsch PW. BERing the burden of damage: Pathway crosstalk and posttranslational modification of base excision repair proteins regulate DNA damage management. DNA Repair (Amst) 2017. [PMID: 28629773 DOI: 10.1016/j.dnarep.2017.06.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
DNA base damage and non-coding apurinic/apyrimidinic (AP) sites are ubiquitous types of damage that must be efficiently repaired to prevent mutations. These damages can occur in both the nuclear and mitochondrial genomes. Base excision repair (BER) is the frontline pathway for identifying and excising damaged DNA bases in both of these cellular compartments. Recent advances demonstrate that BER does not operate as an isolated pathway but rather dynamically interacts with components of other DNA repair pathways to modulate and coordinate BER functions. We define the coordination and interaction between DNA repair pathways as pathway crosstalk. Numerous BER proteins are modified and regulated by post-translational modifications (PTMs), and PTMs could influence pathway crosstalk. Here, we present recent advances on BER/DNA repair pathway crosstalk describing specific examples and also highlight regulation of BER components through PTMs. We have organized and reported functional interactions and documented PTMs for BER proteins into a consolidated summary table. We further propose the concept of DNA repair hubs that coordinate DNA repair pathway crosstalk to identify central protein targets that could play a role in designing future drug targets.
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Affiliation(s)
- Kristin L Limpose
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA, 30322, United States
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA, 30322, United States; Winship Cancer Institute, Emory University, Atlanta, GA 30322, United States.
| | - Paul W Doetsch
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA, 30322, United States; Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, 30322, United States; Winship Cancer Institute, Emory University, Atlanta, GA 30322, United States; Department of Biochemistry, Emory University, Atlanta, GA, 30322, United States.
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5
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Swartzlander DB, McPherson AJ, Powers HR, Limpose KL, Kuiper EG, Degtyareva NP, Corbett AH, Doetsch PW. Identification of SUMO modification sites in the base excision repair protein, Ntg1. DNA Repair (Amst) 2016; 48:51-62. [PMID: 27839712 DOI: 10.1016/j.dnarep.2016.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 12/19/2022]
Abstract
DNA damaging agents are a constant threat to genomes in both the nucleus and the mitochondria. To combat this threat, a suite of DNA repair pathways cooperate to repair numerous types of DNA damage. If left unrepaired, these damages can result in the accumulation of mutations which can lead to deleterious consequences including cancer and neurodegenerative disorders. The base excision repair (BER) pathway is highly conserved from bacteria to humans and is primarily responsible for the removal and subsequent repair of toxic and mutagenic oxidative DNA lesions. Although the biochemical steps that occur in the BER pathway have been well defined, little is known about how the BER machinery is regulated. The budding yeast, Saccharomyces cerevisiae is a powerful model system to biochemically and genetically dissect BER. BER is initiated by DNA N-glycosylases, such as S. cerevisiae Ntg1. Previous work demonstrates that Ntg1 is post-translationally modified by SUMO in response to oxidative DNA damage suggesting that this modification could modulate the function of Ntg1. In this study, we mapped the specific sites of SUMO modification within Ntg1 and identified the enzymes responsible for sumoylating/desumoylating Ntg1. Using a non-sumoylatable version of Ntg1, ntg1ΔSUMO, we performed an initial assessment of the functional impact of Ntg1 SUMO modification in the cellular response to DNA damage. Finally, we demonstrate that, similar to Ntg1, the human homologue of Ntg1, NTHL1, can also be SUMO-modified in response to oxidative stress. Our results suggest that SUMO modification of BER proteins could be a conserved mechanism to coordinate cellular responses to DNA damage.
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Affiliation(s)
- Daniel B Swartzlander
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States; Graduate Program in Genetics and Molecular Biology, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Annie J McPherson
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States; Graduate Program in Genetics and Molecular Biology, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Harry R Powers
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Kristin L Limpose
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States; Graduate Program in Cancer Biology, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Emily G Kuiper
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States; Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Natalya P Degtyareva
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States; Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States; Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, United States.
| | - Paul W Doetsch
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States; Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, United States; Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, United States; Department of Hematology and Medical Oncology Emory University School of Medicine, Atlanta, GA 30322, United States.
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6
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Ishak L, Moretton A, Garreau-Balandier I, Lefebvre M, Alziari S, Lachaume P, Morel F, Farge G, Vernet P, Dubessay P. DNA maintenance following bleomycin-induced strand breaks does not require poly(ADP-ribosyl)ation activation in Drosophila S2 cells. DNA Repair (Amst) 2016; 48:8-16. [PMID: 27793508 DOI: 10.1016/j.dnarep.2016.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 09/05/2016] [Accepted: 10/09/2016] [Indexed: 11/16/2022]
Abstract
BACKGROUND Poly-ADP ribosylation (PARylation) is a post translational modification, catalyzed by Poly(ADP-ribose)polymerase (PARP) family. In Drosophila, PARP-I (human PARP-1 ortholog) is considered to be the only enzymatically active isoform. PARylation is involved in various cellular processes such as DNA repair in case of base excision and strand-breaks. OBSERVATIONS Strand-breaks (SSB and DSB) are detrimental to cell viability and, in Drosophila, that has a unique PARP family organization, little is known on PARP involvement in the control of strand-breaks repair process. In our study, strands-breaks (SSB and DSB) are chemically induced in S2 Drosophila cells using bleomycin. These breaks are efficiently repaired in S2 cells. During the bleomycin treatment, changes in PARylation levels are only detectable in a few cells, and an increase in PARP-I and PARP-II mRNAs is only observed during the recovery period. These results differ strongly from those obtained with Human cells, where PARylation is strongly activating when DNA breaks are generated. Finally, in PARP knock-down cells, DNA stability is altered but no change in strand-breaks repair can be observed. CONCLUSIONS PARP responses in DNA strands-breaks context are functional in Drosophila model as demonstrated by PARP-I and PARP-II mRNA increases. However, no modification of the global PARylation profile is observed during strand-breaks generation, only changes at cellular levels are detectable. Taking together, these results demonstrate that PARylation process in Drosophila is tightly regulated in the context of strands-breaks repair and that PARP is essential during the maintenance of DNA integrity but dispensable in the DNA repair process.
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Affiliation(s)
- Layal Ishak
- Université Clermont Auvergne, Université Blaise Pascal, EA 4645, Réparation du Génome Mitochondrial Normal et Pathologique, BP 10448, F-63000 Clermont-Ferrand, France
| | - Amandine Moretton
- Université Clermont Auvergne, Université Blaise Pascal, EA 4645, Réparation du Génome Mitochondrial Normal et Pathologique, BP 10448, F-63000 Clermont-Ferrand, France
| | - Isabelle Garreau-Balandier
- Université Clermont Auvergne, Université Blaise Pascal, EA 4645, Réparation du Génome Mitochondrial Normal et Pathologique, BP 10448, F-63000 Clermont-Ferrand, France
| | - Mathilde Lefebvre
- Université Clermont Auvergne, Université Blaise Pascal, EA 4645, Réparation du Génome Mitochondrial Normal et Pathologique, BP 10448, F-63000 Clermont-Ferrand, France
| | - Serge Alziari
- Université Clermont Auvergne, Université Blaise Pascal, EA 4645, Réparation du Génome Mitochondrial Normal et Pathologique, BP 10448, F-63000 Clermont-Ferrand, France
| | - Philippe Lachaume
- Université Clermont Auvergne, Université Blaise Pascal, EA 4645, Réparation du Génome Mitochondrial Normal et Pathologique, BP 10448, F-63000 Clermont-Ferrand, France
| | - Frédéric Morel
- Université Clermont Auvergne, Université Blaise Pascal, EA 4645, Réparation du Génome Mitochondrial Normal et Pathologique, BP 10448, F-63000 Clermont-Ferrand, France
| | - Géraldine Farge
- Université Clermont Auvergne, Université Blaise Pascal, EA 4645, Réparation du Génome Mitochondrial Normal et Pathologique, BP 10448, F-63000 Clermont-Ferrand, France
| | - Patrick Vernet
- Université Clermont Auvergne, Université Blaise Pascal, EA 4645, Réparation du Génome Mitochondrial Normal et Pathologique, BP 10448, F-63000 Clermont-Ferrand, France.
| | - Pascal Dubessay
- Université Clermont Auvergne, Université Blaise Pascal, EA 4645, Réparation du Génome Mitochondrial Normal et Pathologique, BP 10448, F-63000 Clermont-Ferrand, France
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7
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Tang W, Zhang M, Li W, Zeng X. An electrochemical sensor based on polyaniline for monitoring hydroquinone and its damage on DNA. Talanta 2014; 127:262-8. [DOI: 10.1016/j.talanta.2014.03.069] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 03/27/2014] [Accepted: 03/29/2014] [Indexed: 12/28/2022]
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8
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Clark N, Wu X, Her C. MutS Homologues hMSH4 and hMSH5: Genetic Variations, Functions, and Implications in Human Diseases. Curr Genomics 2013; 14:81-90. [PMID: 24082819 PMCID: PMC3637681 DOI: 10.2174/1389202911314020002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 01/19/2013] [Accepted: 01/21/2013] [Indexed: 12/01/2022] Open
Abstract
The prominence of the human mismatch repair (MMR) pathway is clearly reflected by the causal link between MMR gene mutations and the occurrence of Lynch syndrome (or HNPCC). The MMR family of proteins also carries out a plethora of diverse cellular functions beyond its primary role in MMR and homologous recombination. In fact, members of the MMR family of proteins are being increasingly recognized as critical mediators between DNA damage repair and cell survival. Thus, a better functional understanding of MMR proteins will undoubtedly aid the development of strategies to effectively enhance apoptotic signaling in response to DNA damage induced by anti-cancer therapeutics. Among the five known human MutS homologs, hMSH4 and hMSH5 form a unique heterocomplex. However, the expression profiles of the two genes are not correlated in a number of cell types, suggesting that they may function independently as well. Consistent with this, these two proteins are promiscuous and thought to play distinct roles through interacting with different binding partners. Here, we describe the gene and protein structures of eukaryotic MSH4 and MSH5 with a particular emphasis on their human homologues, and we discuss recent findings of the roles of these two genes in DNA damage response and repair. Finally, we delineate the potential links of single nucleotide polymorphism (SNP) loci of these two genes with several human diseases.
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Affiliation(s)
- Nicole Clark
- STARS Program, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-7520, USA ; School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-7520, USA
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9
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Kavanagh JN, Redmond KM, Schettino G, Prise KM. DNA double strand break repair: a radiation perspective. Antioxid Redox Signal 2013; 18:2458-72. [PMID: 23311752 DOI: 10.1089/ars.2012.5151] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SIGNIFICANCE Ionizing radiation (IR) can induce a wide range of unique deoxyribonucleic acid (DNA) lesions due to the spatiotemporal correlation of the ionization produced. Of these, DNA double strand breaks (DSBs) play a key role. Complex mechanisms and sophisticated pathways are available within cells to restore the integrity and sequence of the damaged DNA molecules. RECENT ADVANCES Here we review the main aspects of the DNA DSB repair mechanisms with emphasis on the molecular pathways, radiation-induced lesions, and their significance for cellular processes. CRITICAL ISSUES Although the main characteristics and proteins involved in the two DNA DSB repair processes present in eukaryotic cells (homologous recombination and nonhomologous end-joining) are reasonably well established, there are still uncertainties regarding the primary sensing event and their dependency on the complexity, location, and time of the damage. Interactions and overlaps between the different pathways play a critical role in defining the repair efficiency and determining the cellular functional behavior due to unrepaired/miss-repaired DNA lesions. The repair pathways involved in repairing lesions induced by soluble factors released from directly irradiated cells may also differ from the established response mechanisms. FUTURE DIRECTIONS An improved understanding of the molecular pathways involved in sensing and repairing damaged DNA molecules and the role of DSBs is crucial for the development of novel classes of drugs to treat human diseases and to exploit characteristics of IR and alterations in tumor cells for successful radiotherapy applications.
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Affiliation(s)
- Joy N Kavanagh
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, United Kingdom
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10
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Fenton AL, Shirodkar P, Macrae CJ, Meng L, Koch CA. The PARP3- and ATM-dependent phosphorylation of APLF facilitates DNA double-strand break repair. Nucleic Acids Res 2013; 41:4080-92. [PMID: 23449221 PMCID: PMC3627606 DOI: 10.1093/nar/gkt134] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
APLF is a forkhead associated-containing protein with poly(ADP-ribose)-binding zinc finger (PBZ) domains, which undergoes ionizing radiation (IR)-induced and Ataxia-Telangiectasia Mutated (ATM)-dependent phosphorylation at serine-116 (Ser(116)). Here, we demonstrate that the phosphorylation of APLF at Ser(116) in human U2OS cells by ATM is dependent on poly(ADP-ribose) polymerase 3 (PARP3) levels and the APLF PBZ domains. The interaction of APLF at sites of DNA damage was diminished by the single substitution of APLF Ser(116) to alanine, and the cellular depletion or chemical inhibition of ATM or PARP3 also altered the level of accumulation of APLF at sites of laser-induced DNA damage and impaired the accumulation of Ser(116)-phosphorylated APLF at IR-induced γH2AX foci in human cells. The data further suggest that ATM and PARP3 participate in a common signalling pathway to facilitate APLF-Ser(116) phosphorylation, which, in turn, appears to be required for efficient DNA double-strand break repair kinetics and cell survival following IR. Collectively, these findings provide a more detailed understanding of the molecular pathway that leads to the phosphorylation of APLF following DNA damage and suggest that Ser(116)-APLF phosphorylation facilitates APLF-dependent double-strand break repair.
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Affiliation(s)
- Amanda L Fenton
- Division of Signalling Biology, Ontario Cancer Institute (University Health Network), 610 University Avenue, Toronto, Ontario M5G 2M9, Canada
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11
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DNA damage stress response in germ cells: role of c-Abl and clinical implications. Oncogene 2010; 29:6193-202. [PMID: 20818431 DOI: 10.1038/onc.2010.410] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells experiencing DNA damage undergo a complex response entailing cell-cycle arrest, DNA repair and apoptosis, the relative importance of the three being modulated by the extent of the lesion. The observation that Abl interacts in the nucleus with several proteins involved in different aspects of DNA repair has led to the hypothesis that this kinase is part of the damage-sensing mechanism. However, the mechanistic details underlying the role of Abl in DNA repair remain unclear. Here, I will review the evidence supporting our current understanding of Abl activation following DNA insults, while focusing on the relevance of these mechanisms in protecting DNA-injured germ cells. Early studies have shown that Abl transcripts are highly expressed in the germ line. Abl-deficient mice exhibit multiple abnormalities, increased perinatal mortality and reduced fertility. Recent findings have implicated Abl in a cisplatin-induced signaling pathway eliciting death of immature oocytes. A p53-related protein, TAp63, is an important immediate downstream effector of this pathway. Of note, pharmacological inhibition of Abl protects the ovarian reserve from the toxic effects of cisplatin. This suggests that the extent of Abl catalytic outputs may shift the balance between survival (likely through DNA repair) and activation of a death response. Taken together, these observations are consistent with the evolutionary conserved relationship between DNA damage and activation of the p53 family of transcription factors, while shedding light on the key role of Abl in dictating the fate of germ cells upon genotoxic insults.
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12
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Mistry H, Tamblyn L, Butt H, Sisgoreo D, Gracias A, Larin M, Gopalakrishnan K, Hande MP, McPherson JP. UHRF1 is a genome caretaker that facilitates the DNA damage response to gamma-irradiation. Genome Integr 2010; 1:7. [PMID: 20678257 PMCID: PMC2914011 DOI: 10.1186/2041-9414-1-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 06/08/2010] [Indexed: 11/10/2022] Open
Abstract
Background DNA double-strand breaks (DSBs) caused by ionizing radiation or by the stalling of DNA replication forks are among the most deleterious forms of DNA damage. The ability of cells to recognize and repair DSBs requires post-translational modifications to histones and other proteins that facilitate access to lesions in compacted chromatin, however our understanding of these processes remains incomplete. UHRF1 is an E3 ubiquitin ligase that has previously been linked to events that regulate chromatin remodeling and epigenetic maintenance. Previous studies have demonstrated that loss of UHRF1 increases the sensitivity of cells to DNA damage however the role of UHRF1 in this response is unclear. Results We demonstrate that UHRF1 plays a critical role for facilitating the response to DSB damage caused by γ-irradiation. UHRF1-depleted cells exhibit increased sensitivity to γ-irradiation, suggesting a compromised cellular response to DSBs. UHRF1-depleted cells show impaired cell cycle arrest and an impaired accumulation of histone H2AX phosphorylation (γH2AX) in response to γ-irradiation compared to control cells. We also demonstrate that UHRF1 is required for genome integrity, in that UHRF1-depleted cells displayed an increased frequency of chromosomal aberrations compared to control cells. Conclusions Our findings indicate a critical role for UHRF1 in maintenance of chromosome integrity and an optimal response to DSB damage.
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Affiliation(s)
- Helena Mistry
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5 S 1A8, Canada
| | - Laura Tamblyn
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5 S 1A8, Canada
| | - Hussein Butt
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5 S 1A8, Canada
| | - Daniel Sisgoreo
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5 S 1A8, Canada
| | - Aileen Gracias
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5 S 1A8, Canada
| | - Meghan Larin
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5 S 1A8, Canada
| | - Kalpana Gopalakrishnan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Manoor Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - John Peter McPherson
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5 S 1A8, Canada
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13
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Silva JP, Gomes AC, Proença F, Coutinho OP. Novel nitrogen compounds enhance protection and repair of oxidative DNA damage in a neuronal cell model: Comparison with quercetin. Chem Biol Interact 2009; 181:328-37. [DOI: 10.1016/j.cbi.2009.07.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Revised: 07/29/2009] [Accepted: 07/29/2009] [Indexed: 11/24/2022]
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14
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Roques C, Coulombe Y, Delannoy M, Vignard J, Grossi S, Brodeur I, Rodrigue A, Gautier J, Stasiak AZ, Stasiak A, Constantinou A, Masson JY. MRE11-RAD50-NBS1 is a critical regulator of FANCD2 stability and function during DNA double-strand break repair. EMBO J 2009; 28:2400-13. [PMID: 19609304 PMCID: PMC2735166 DOI: 10.1038/emboj.2009.193] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 06/17/2009] [Indexed: 01/04/2023] Open
Abstract
Monoubiquitination of the Fanconi anaemia protein FANCD2 is a key event leading to repair of interstrand cross-links. It was reported earlier that FANCD2 co-localizes with NBS1. However, the functional connection between FANCD2 and MRE11 is poorly understood. In this study, we show that inhibition of MRE11, NBS1 or RAD50 leads to a destabilization of FANCD2. FANCD2 accumulated from mid-S to G2 phase within sites containing single-stranded DNA (ssDNA) intermediates, or at sites of DNA damage, such as those created by restriction endonucleases and laser irradiation. Purified FANCD2, a ring-like particle by electron microscopy, preferentially bound ssDNA over various DNA substrates. Inhibition of MRE11 nuclease activity by Mirin decreased the number of FANCD2 foci formed in vivo. We propose that FANCD2 binds to ssDNA arising from MRE11-processed DNA double-strand breaks. Our data establish MRN as a crucial regulator of FANCD2 stability and function in the DNA damage response.
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Affiliation(s)
- Céline Roques
- Genome Stability Laboratory, Laval University Cancer Research Center, Hôtel-Dieu de Québec, Québec, Canada
| | - Yan Coulombe
- Genome Stability Laboratory, Laval University Cancer Research Center, Hôtel-Dieu de Québec, Québec, Canada
| | - Mathieu Delannoy
- Department of Biochemistry, University of Lausanne, BIL Biomedical Research Center, Lausanne, Switzerland
| | - Julien Vignard
- Genome Stability Laboratory, Laval University Cancer Research Center, Hôtel-Dieu de Québec, Québec, Canada
| | - Simona Grossi
- Department of Biochemistry, University of Lausanne, BIL Biomedical Research Center, Lausanne, Switzerland
| | - Isabelle Brodeur
- Genome Stability Laboratory, Laval University Cancer Research Center, Hôtel-Dieu de Québec, Québec, Canada
| | - Amélie Rodrigue
- Genome Stability Laboratory, Laval University Cancer Research Center, Hôtel-Dieu de Québec, Québec, Canada
| | - Jean Gautier
- Columbia University, Institute for Cancer Genetics, Irving Cancer Research Center, New York, NY, USA
| | - Alicja Z Stasiak
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Andrzej Stasiak
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Angelos Constantinou
- Department of Biochemistry, University of Lausanne, BIL Biomedical Research Center, Lausanne, Switzerland
| | - Jean-Yves Masson
- Genome Stability Laboratory, Laval University Cancer Research Center, Hôtel-Dieu de Québec, Québec, Canada
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15
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Tompkins JD, Wu X, Chu YL, Her C. Evidence for a direct involvement of hMSH5 in promoting ionizing radiation induced apoptosis. Exp Cell Res 2009; 315:2420-32. [PMID: 19442657 DOI: 10.1016/j.yexcr.2009.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 04/06/2009] [Accepted: 05/06/2009] [Indexed: 10/20/2022]
Abstract
Although increasing evidence has suggested that the hMSH5 protein plays an important role in meiotic and mitotic DNA recombinational repair, its precise functions in recombination and DNA damage response are presently elusive. Here we show that the interaction between hMSH5 and c-Abl confers ionizing radiation (IR)-induced apoptotic response by promoting c-Abl activation and p73 accumulation, and these effects are greatly enhanced in cells expressing hMSH5(P29S) (i.e. the hMSH5 variant possessing a proline to serine change within the N-terminal (Px)(5) dipeptide repeat). Our current study provides the first evidence that the (Px)(5) dipeptide repeat plays an important role in modulating the interaction between hMSH5 and c-Abl and alteration of this dipeptide repeat in hMSH5(P29S) leads to increased IR sensitivity owing to enhanced caspase-3-mediated apoptosis. In addition, RNAi-mediated hMSH5 silencing leads to the reduction of apoptosis in IR-treated cells. In short, this study implicates a role for hMSH5 in DNA damage response involving c-Abl and p73, and suggests that mutations impairing this process could significantly affect normal cellular responses to anti-cancer treatments.
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Affiliation(s)
- Joshua D Tompkins
- School of Molecular Biosciences and Center for Reproductive Biology, PO Box 644660, Washington State University, Pullman, WA 99164-4660, USA
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16
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Brown JB, Akutsu T. Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology. BMC Bioinformatics 2009; 10:25. [PMID: 19154573 PMCID: PMC2660303 DOI: 10.1186/1471-2105-10-25] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 01/20/2009] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND DNA repair is the general term for the collection of critical mechanisms which repair many forms of DNA damage such as methylation or ionizing radiation. DNA repair has mainly been studied in experimental and clinical situations, and relatively few information-based approaches to new extracting DNA repair knowledge exist. As a first step, automatic detection of DNA repair proteins in genomes via informatics techniques is desirable; however, there are many forms of DNA repair and it is not a straightforward process to identify and classify repair proteins with a single optimal method. We perform a study of the ability of homology and machine learning-based methods to identify and classify DNA repair proteins, as well as scan vertebrate genomes for the presence of novel repair proteins. Combinations of primary sequence polypeptide frequency, secondary structure, and homology information are used as feature information for input to a Support Vector Machine (SVM). RESULTS We identify that SVM techniques are capable of identifying portions of DNA repair protein datasets without admitting false positives; at low levels of false positive tolerance, homology can also identify and classify proteins with good performance. Secondary structure information provides improved performance compared to using primary structure alone. Furthermore, we observe that machine learning methods incorporating homology information perform best when data is filtered by some clustering technique. Analysis by applying these methodologies to the scanning of multiple vertebrate genomes confirms a positive correlation between the size of a genome and the number of DNA repair protein transcripts it is likely to contain, and simultaneously suggests that all organisms have a non-zero minimum number of repair genes. In addition, the scan result clusters several organisms' repair abilities in an evolutionarily consistent fashion. Analysis also identifies several functionally unconfirmed proteins that are highly likely to be involved in the repair process. A new web service, INTREPED, has been made available for the immediate search and annotation of DNA repair proteins in newly sequenced genomes. CONCLUSION Despite complexity due to a multitude of repair pathways, combinations of sequence, structure, and homology with Support Vector Machines offer good methods in addition to existing homology searches for DNA repair protein identification and functional annotation. Most importantly, this study has uncovered relationships between the size of a genome and a genome's available repair repertoire, and offers a number of new predictions as well as a prediction service, both which reduce the search time and cost for novel repair genes and proteins.
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Affiliation(s)
- J B Brown
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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17
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Yang Z, Waldman AS, Wyatt MD. DNA damage and homologous recombination signaling induced by thymidylate deprivation. Biochem Pharmacol 2008; 76:987-96. [PMID: 18773878 DOI: 10.1016/j.bcp.2008.08.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 08/05/2008] [Accepted: 08/07/2008] [Indexed: 02/03/2023]
Abstract
DNA damage is accepted as a consequence of thymidylate deprivation induced by chemotherapeutic inhibitors of thymidylate synthase (TS), but the types of damage and signaling responses remain incompletely understood. Thymidylate deprivation increases dUTP and uracil in DNA, which is removed by base excision repair (BER). Because BER requires a synthesis step, strand break intermediates presumably accumulate. Thymidylate deprivation also induces cell cycle arrest during replication. Homologous recombination (HR) is a means of repairing persistent BER intermediates and collapsed replication forks. There are also intimate links between HR and S-phase checkpoint pathways. In this study, the goals were to determine the involvement of HR-associated proteins and DNA damage signaling responses to thymidylate deprivation. When RAD51, which is a central component of HR, was depleted by siRNA cells were sensitized to raltitrexed (RTX), which specifically inhibits TS. To our knowledge, this is the first demonstration in mammalian cells that depletion of RAD51 causes sensitivity to thymidylate deprivation. Activation of DNA damage signaling responses was examined following treatment with RTX. Phosphorylation of replication protein A (RPA2 subunit) and formation of damage-induced foci were strikingly evident following IC(50) doses of RTX. Induction was much more striking following RTX treatment than with hydroxyurea, which is commonly used to inhibit replication. RTX treatment also induced foci of RAD51, gamma-H2AX, phospho-Chk1, and phospho-NBS1, although the extent of co-localization with RPA2 foci varied. Collectively, the results suggest that HR and S-phase checkpoint signaling processes are invoked by thymidylate deprivation and influence cellular resistance to thymidylate deprivation.
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Affiliation(s)
- Zhengguan Yang
- Department of Pharmaceutical and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
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18
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Schroering AG, Williams KJ. Rapid induction of chromatin-associated DNA mismatch repair proteins after MNNG treatment. DNA Repair (Amst) 2008; 7:951-69. [PMID: 18468964 DOI: 10.1016/j.dnarep.2008.03.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Revised: 03/07/2008] [Accepted: 03/23/2008] [Indexed: 12/18/2022]
Abstract
Treatment with low concentrations of monofunctional alkylating agents induces a G2 arrest only after the second round of DNA synthesis in mammalian cells and requires a proficient mismatch repair (MMR) pathway. Here, we have investigated rapid alkylation-induced recruitment of DNA repair proteins to chromosomal DNA within synchronized populations of MMR proficient cells (HeLa MR) after N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) treatment. Within the first hour, the concentrations of MutS alpha and PCNA increase well beyond their constitutive chromosomally bound levels and MutL alpha is newly recruited to the chromatin-bound MutS alpha. Remarkably, immunoprecipitation experiments demonstrate rapid association of these proteins on the alkylation-damaged chromatin, even when DNA replication is completely blocked. The extent of association of PCNA and MMR proteins on the chromatin is dependent upon the concentration of MNNG and on the specific type of replication block. A subpopulation of the MutS alpha-associated PCNA also becomes monoubiquitinated, a known requirement for PCNA to interact with translesion synthesis (TLS) polymerases. In addition, chromatin-bound SMC1 and NBS1 proteins, associated with DNA double-strand-breaks (DSBs), become phosphorylated within 1-2h of exposure to MNNG. However, these activated proteins are not co-localized on the chromatin with MutS alpha in response to MNNG exposure. PCNA, MutS alpha/MutL alpha and activated SMC1/NBS1 remain chromatin-bound for at least 6-8h after alkylation damage. Thus, cells that are exposed to low levels of alkylation treatment undergo rapid recruitment to and/or activation of key proteins already on the chromatin without the requirement for DNA replication, apparently via different DNA-damage signaling pathways.
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Affiliation(s)
- Allen G Schroering
- University of Toledo College of Medicine, Health Science Campus, Department of Biochemistry & Cancer Biology, Toledo, OH 43614, USA
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19
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Wang GG, Allis CD, Chi P. Chromatin remodeling and cancer, Part I: Covalent histone modifications. Trends Mol Med 2007; 13:363-72. [PMID: 17822958 DOI: 10.1016/j.molmed.2007.07.003] [Citation(s) in RCA: 266] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Revised: 06/30/2007] [Accepted: 07/04/2007] [Indexed: 12/12/2022]
Abstract
Dynamic chromatin remodeling underlies many, if not all, DNA-templated biological processes, including gene transcription; DNA replication and repair; chromosome condensation; and segregation and apoptosis. Disruption of these processes has been linked to the development and progression of cancer. The mechanisms of dynamic chromatin remodeling include the use of covalent histone modifications, histone variants, ATP-dependent complexes and DNA methylation. Together, these mechanisms impart variation into the chromatin fiber, and this variation gives rise to an 'epigenetic landscape' that extends the biological output of DNA alone. Here, we review recent advances in chromatin remodeling, and pay particular attention to mechanisms that appear to be linked to human cancer. Where possible, we discuss the implications of these advances for disease-management strategies.
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Affiliation(s)
- Gang G Wang
- Laboratory of Chromatin Biology, The Rockefeller University, and Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
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